- PDB-4rs6: Crystal structure of the C domain of Polo like Kinase II in Homo ... -
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Basic information
Entry
Database: PDB / ID: 4rs6
Title
Crystal structure of the C domain of Polo like Kinase II in Homo Sapiens
Components
Serine/threonine-protein kinase PLK2
Keywords
TRANSFERASE / First PBD domain of Polo like Kinase II / phosphorylation of target protein
Function / homology
Function and homology information
regulation of centriole replication / Rap protein signal transduction / negative regulation of apoptotic process in bone marrow cell / polo kinase / ATP-dependent protein binding / long-term synaptic depression / CD163 mediating an anti-inflammatory response / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cellular senescence ...regulation of centriole replication / Rap protein signal transduction / negative regulation of apoptotic process in bone marrow cell / polo kinase / ATP-dependent protein binding / long-term synaptic depression / CD163 mediating an anti-inflammatory response / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cellular senescence / positive regulation of autophagy / negative regulation of inflammatory response to antigenic stimulus / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / centriole / negative regulation of angiogenesis / mitotic spindle organization / long-term synaptic potentiation / regulation of synaptic plasticity / memory / kinetochore / spindle pole / G1/S transition of mitotic cell cycle / positive regulation of protein catabolic process / peptidyl-serine phosphorylation / positive regulation of canonical NF-kappaB signal transduction / Ras protein signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / chromatin / negative regulation of apoptotic process / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function
PLK2, catalytic domain / POLO box domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / Serine/threonine-protein kinase, active site ...PLK2, catalytic domain / POLO box domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2.6→24.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 22.591 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.478 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24724
947
5.1 %
RANDOM
Rwork
0.18595
-
-
-
obs
0.18891
17518
99.83 %
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all
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18474
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-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 71.497 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→24.83 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3448
0
0
14
3462
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.019
3528
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3280
X-RAY DIFFRACTION
r_angle_refined_deg
1.737
1.953
4782
X-RAY DIFFRACTION
r_angle_other_deg
0.888
3
7550
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.788
5
424
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.105
24.471
170
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.87
15
614
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.173
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.107
0.2
530
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
3978
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
838
LS refinement shell
Resolution: 2.6→2.667 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.39
82
-
Rwork
0.317
1236
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
4.5673
0.4476
1.978
2.8431
0.1465
6.6787
-0.0785
0.0737
-0.4352
0.2101
0.2908
-0.0432
-0.094
0.1769
-0.2123
0.0827
-0.0347
0.0631
0.0869
-0.0219
0.2303
-19.1653
-55.0548
-10.6011
2
5.6622
2.8236
-3.3081
6.6431
-3.2224
4.156
-0.0896
0.1874
0.4722
0.1234
0.3788
0.236
-0.2637
-0.4921
-0.2892
0.237
0.0769
-0.023
0.1812
0.1004
0.1146
-38.2322
-33.4712
-3.3083
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
470 - 682
2
X-RAY DIFFRACTION
2
B
470 - 682
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